data_8IY0 # _model_server_result.job_id Atrtltw9b_lJSpRQcfeplw _model_server_result.datetime_utc '2024-11-23 21:17:54' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 8iy0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":103}' # _entry.id 8IY0 # _exptl.entry_id 8IY0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' _entity.pdbx_number_of_molecules 18 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 8IY0 _cell.length_a 103.904 _cell.length_b 103.904 _cell.length_c 101.864 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8IY0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 ? hexameric 6 author_defined_assembly 3 ? hexameric 6 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,H,I,Y 1 1 A,G,H,I,Y 1 2 A,G,H,I,Y 1 4 A,G,H,I,Y 1 6 A,G,H,I,Y 1 8 A,G,H,I,Y 1 10 B,J,K,L,Z 2 1 B,J,K,L,Z 2 2 B,J,K,L,Z 2 4 B,J,K,L,Z 2 7 B,J,K,L,Z 2 9 B,J,K,L,Z 2 11 C,D,M,N,O,P,Q,R,AA,BA 3 1 C,D,M,N,O,P,Q,R,AA,BA 3 3 C,D,M,N,O,P,Q,R,AA,BA 3 5 E,F,S,T,U,V,W,X,CA,DA 4 1 E,F,S,T,U,V,W,X,CA,DA 4 3 E,F,S,T,U,V,W,X,CA,DA 4 5 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 103.904 0 0 4 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.952 89.983504 0 6 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 101.864 7 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 101.864 9 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 10 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 101.864 11 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X N N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id 3AM _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "3'-AMP" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O1P P 3AM doub 1 n n P O2P 3AM sing 2 n n P O3P 3AM sing 3 n n P O3' 3AM sing 4 n n O2' C2' 3AM sing 5 n n C2' C3' 3AM sing 6 n n C2' C1' 3AM sing 7 n n C3' O3' 3AM sing 8 n n C3' C4' 3AM sing 9 n n C1' O4' 3AM sing 10 n n C1' N9 3AM sing 11 n n O4' C4' 3AM sing 12 n n C4' C5' 3AM sing 13 n n C5' O5' 3AM sing 14 n n N9 C8 3AM sing 15 n y N9 C4 3AM sing 16 n y C8 N7 3AM doub 17 n y N7 C5 3AM sing 18 n y C5 C6 3AM doub 19 n y C5 C4 3AM sing 20 n y C6 N6 3AM sing 21 n n C6 N1 3AM sing 22 n y C4 N3 3AM doub 23 n y N3 C2 3AM sing 24 n y C2 N1 3AM doub 25 n y O2P HO2P 3AM sing 26 n n O3P HO3P 3AM sing 27 n n O2' HO2' 3AM sing 28 n n C2' H2' 3AM sing 29 n n C3' H3' 3AM sing 30 n n C1' H1' 3AM sing 31 n n C4' H4' 3AM sing 32 n n C5' H5' 3AM sing 33 n n C5' "H5'A" 3AM sing 34 n n O5' HO5' 3AM sing 35 n n C8 H8 3AM sing 36 n n N6 HN6 3AM sing 37 n n N6 HN6A 3AM sing 38 n n C2 H2 3AM sing 39 n n # _atom_sites.entry_id 8IY0 _atom_sites.fract_transf_matrix[1][1] 0.009624 _atom_sites.fract_transf_matrix[1][2] 0.005557 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011113 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009817 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code G 2 3AM A 1 101 101 3AM AAA . H 2 3AM A 1 102 101 3AM AAA . I 2 3AM A 1 103 101 3AM AAA . J 2 3AM B 1 101 101 3AM AAA . K 2 3AM B 1 102 101 3AM AAA . L 2 3AM B 1 103 101 3AM AAA . M 2 3AM C 1 101 101 3AM AAA . N 2 3AM C 1 102 101 3AM AAA . O 2 3AM C 1 103 101 3AM AAA . P 2 3AM D 1 101 101 3AM AAA . Q 2 3AM D 1 102 101 3AM AAA . R 2 3AM D 1 103 101 3AM AAA . S 2 3AM E 1 101 101 3AM AAA . T 2 3AM E 1 102 101 3AM AAA . U 2 3AM E 1 103 101 3AM AAA . V 2 3AM F 1 101 101 3AM AAA . W 2 3AM F 1 102 101 3AM AAA . X 2 3AM F 1 103 101 3AM AAA . Y 3 HOH A 1 201 57 HOH HOH . Y 3 HOH A 2 202 87 HOH HOH . Y 3 HOH A 3 203 144 HOH HOH . Y 3 HOH A 4 204 15 HOH HOH . Y 3 HOH A 5 205 51 HOH HOH . Y 3 HOH A 6 206 4 HOH HOH . Y 3 HOH A 7 207 14 HOH HOH . Y 3 HOH A 8 208 163 HOH HOH . Y 3 HOH A 9 209 13 HOH HOH . Y 3 HOH A 10 210 8 HOH HOH . Y 3 HOH A 11 211 103 HOH HOH . Y 3 HOH A 12 212 170 HOH HOH . Y 3 HOH A 13 213 61 HOH HOH . Y 3 HOH A 14 214 21 HOH HOH . Y 3 HOH A 15 215 26 HOH HOH . Y 3 HOH A 16 216 65 HOH HOH . Y 3 HOH A 17 217 17 HOH HOH . Y 3 HOH A 18 218 168 HOH HOH . Y 3 HOH A 19 219 179 HOH HOH . Y 3 HOH A 20 220 71 HOH HOH . Y 3 HOH A 21 221 48 HOH HOH . Y 3 HOH A 22 222 66 HOH HOH . Y 3 HOH A 23 223 2 HOH HOH . Y 3 HOH A 24 224 109 HOH HOH . Y 3 HOH A 25 225 172 HOH HOH . Y 3 HOH A 26 226 76 HOH HOH . Y 3 HOH A 27 227 52 HOH HOH . Y 3 HOH A 28 228 42 HOH HOH . Y 3 HOH A 29 229 12 HOH HOH . Y 3 HOH A 30 230 78 HOH HOH . Y 3 HOH A 31 231 181 HOH HOH . Y 3 HOH A 32 232 177 HOH HOH . Y 3 HOH A 33 233 88 HOH HOH . Y 3 HOH A 34 234 119 HOH HOH . Y 3 HOH A 35 235 67 HOH HOH . Y 3 HOH A 36 236 1 HOH HOH . Y 3 HOH A 37 237 142 HOH HOH . Y 3 HOH A 38 238 101 HOH HOH . Y 3 HOH A 39 239 27 HOH HOH . Y 3 HOH A 40 240 37 HOH HOH . Y 3 HOH A 41 241 82 HOH HOH . Y 3 HOH A 42 242 62 HOH HOH . Y 3 HOH A 43 243 56 HOH HOH . Y 3 HOH A 44 244 110 HOH HOH . Y 3 HOH A 45 245 23 HOH HOH . Y 3 HOH A 46 246 108 HOH HOH . Y 3 HOH A 47 247 162 HOH HOH . Y 3 HOH A 48 248 44 HOH HOH . Y 3 HOH A 49 249 149 HOH HOH . Z 3 HOH B 1 201 111 HOH HOH . Z 3 HOH B 2 202 16 HOH HOH . Z 3 HOH B 3 203 25 HOH HOH . Z 3 HOH B 4 204 89 HOH HOH . Z 3 HOH B 5 205 34 HOH HOH . Z 3 HOH B 6 206 113 HOH HOH . Z 3 HOH B 7 207 180 HOH HOH . Z 3 HOH B 8 208 95 HOH HOH . Z 3 HOH B 9 209 75 HOH HOH . Z 3 HOH B 10 210 148 HOH HOH . Z 3 HOH B 11 211 54 HOH HOH . Z 3 HOH B 12 212 74 HOH HOH . Z 3 HOH B 13 213 59 HOH HOH . Z 3 HOH B 14 214 41 HOH HOH . Z 3 HOH B 15 215 145 HOH HOH . Z 3 HOH B 16 216 153 HOH HOH . Z 3 HOH B 17 217 49 HOH HOH . Z 3 HOH B 18 218 117 HOH HOH . Z 3 HOH B 19 219 139 HOH HOH . Z 3 HOH B 20 220 43 HOH HOH . Z 3 HOH B 21 221 7 HOH HOH . Z 3 HOH B 22 222 171 HOH HOH . Z 3 HOH B 23 223 140 HOH HOH . Z 3 HOH B 24 224 167 HOH HOH . Z 3 HOH B 25 225 35 HOH HOH . Z 3 HOH B 26 226 129 HOH HOH . AA 3 HOH C 1 201 91 HOH HOH . AA 3 HOH C 2 202 160 HOH HOH . AA 3 HOH C 3 203 24 HOH HOH . AA 3 HOH C 4 204 137 HOH HOH . AA 3 HOH C 5 205 55 HOH HOH . AA 3 HOH C 6 206 155 HOH HOH . AA 3 HOH C 7 207 68 HOH HOH . AA 3 HOH C 8 208 31 HOH HOH . AA 3 HOH C 9 209 22 HOH HOH . AA 3 HOH C 10 210 58 HOH HOH . AA 3 HOH C 11 211 30 HOH HOH . AA 3 HOH C 12 212 20 HOH HOH . AA 3 HOH C 13 213 94 HOH HOH . AA 3 HOH C 14 214 84 HOH HOH . AA 3 HOH C 15 215 46 HOH HOH . AA 3 HOH C 16 216 156 HOH HOH . AA 3 HOH C 17 217 176 HOH HOH . AA 3 HOH C 18 218 70 HOH HOH . AA 3 HOH C 19 219 154 HOH HOH . AA 3 HOH C 20 220 134 HOH HOH . AA 3 HOH C 21 221 123 HOH HOH . AA 3 HOH C 22 222 125 HOH HOH . AA 3 HOH C 23 223 128 HOH HOH . AA 3 HOH C 24 224 143 HOH HOH . AA 3 HOH C 25 225 100 HOH HOH . AA 3 HOH C 26 226 105 HOH HOH . AA 3 HOH C 27 227 102 HOH HOH . AA 3 HOH C 28 228 124 HOH HOH . AA 3 HOH C 29 229 157 HOH HOH . BA 3 HOH D 1 201 173 HOH HOH . BA 3 HOH D 2 202 96 HOH HOH . BA 3 HOH D 3 203 92 HOH HOH . BA 3 HOH D 4 204 11 HOH HOH . BA 3 HOH D 5 205 38 HOH HOH . BA 3 HOH D 6 206 47 HOH HOH . BA 3 HOH D 7 207 64 HOH HOH . BA 3 HOH D 8 208 85 HOH HOH . BA 3 HOH D 9 209 133 HOH HOH . BA 3 HOH D 10 210 161 HOH HOH . BA 3 HOH D 11 211 60 HOH HOH . BA 3 HOH D 12 212 164 HOH HOH . BA 3 HOH D 13 213 10 HOH HOH . BA 3 HOH D 14 214 80 HOH HOH . BA 3 HOH D 15 215 18 HOH HOH . BA 3 HOH D 16 216 138 HOH HOH . BA 3 HOH D 17 217 72 HOH HOH . BA 3 HOH D 18 218 126 HOH HOH . BA 3 HOH D 19 219 9 HOH HOH . BA 3 HOH D 20 220 99 HOH HOH . BA 3 HOH D 21 221 93 HOH HOH . BA 3 HOH D 22 222 115 HOH HOH . BA 3 HOH D 23 223 114 HOH HOH . BA 3 HOH D 24 224 40 HOH HOH . BA 3 HOH D 25 225 118 HOH HOH . BA 3 HOH D 26 226 158 HOH HOH . BA 3 HOH D 27 227 3 HOH HOH . BA 3 HOH D 28 228 77 HOH HOH . BA 3 HOH D 29 229 136 HOH HOH . BA 3 HOH D 30 230 5 HOH HOH . BA 3 HOH D 31 231 151 HOH HOH . BA 3 HOH D 32 232 69 HOH HOH . BA 3 HOH D 33 233 112 HOH HOH . BA 3 HOH D 34 234 86 HOH HOH . BA 3 HOH D 35 235 39 HOH HOH . BA 3 HOH D 36 236 104 HOH HOH . CA 3 HOH E 1 201 182 HOH HOH . CA 3 HOH E 2 202 53 HOH HOH . CA 3 HOH E 3 203 169 HOH HOH . CA 3 HOH E 4 204 147 HOH HOH . CA 3 HOH E 5 205 33 HOH HOH . CA 3 HOH E 6 206 178 HOH HOH . CA 3 HOH E 7 207 116 HOH HOH . CA 3 HOH E 8 208 83 HOH HOH . CA 3 HOH E 9 209 130 HOH HOH . CA 3 HOH E 10 210 6 HOH HOH . CA 3 HOH E 11 211 174 HOH HOH . CA 3 HOH E 12 212 150 HOH HOH . CA 3 HOH E 13 213 97 HOH HOH . CA 3 HOH E 14 214 175 HOH HOH . CA 3 HOH E 15 215 183 HOH HOH . CA 3 HOH E 16 216 32 HOH HOH . CA 3 HOH E 17 217 159 HOH HOH . CA 3 HOH E 18 218 50 HOH HOH . CA 3 HOH E 19 219 132 HOH HOH . CA 3 HOH E 20 220 131 HOH HOH . CA 3 HOH E 21 221 135 HOH HOH . CA 3 HOH E 22 222 141 HOH HOH . DA 3 HOH F 1 201 63 HOH HOH . DA 3 HOH F 2 202 29 HOH HOH . DA 3 HOH F 3 203 79 HOH HOH . DA 3 HOH F 4 204 73 HOH HOH . DA 3 HOH F 5 205 45 HOH HOH . DA 3 HOH F 6 206 81 HOH HOH . DA 3 HOH F 7 207 146 HOH HOH . DA 3 HOH F 8 208 165 HOH HOH . DA 3 HOH F 9 209 120 HOH HOH . DA 3 HOH F 10 210 121 HOH HOH . DA 3 HOH F 11 211 90 HOH HOH . DA 3 HOH F 12 212 122 HOH HOH . DA 3 HOH F 13 213 36 HOH HOH . DA 3 HOH F 14 214 166 HOH HOH . DA 3 HOH F 15 215 98 HOH HOH . DA 3 HOH F 16 216 127 HOH HOH . DA 3 HOH F 17 217 106 HOH HOH . DA 3 HOH F 18 218 19 HOH HOH . DA 3 HOH F 19 219 107 HOH HOH . DA 3 HOH F 20 220 152 HOH HOH . DA 3 HOH F 21 221 28 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P P 3AM . . . R 2 51.271 26.212 46.46 0.34 28.51 ? P 3AM 103 D 1 HETATM 2 O O2P 3AM . . . R 2 50.705 24.871 46.848 0.34 26.62 ? O2P 3AM 103 D 1 HETATM 3 O O3P 3AM . . . R 2 51.706 26.469 45.033 0.34 29.61 ? O3P 3AM 103 D 1 HETATM 4 O O2' 3AM . . . R 2 52.557 27.569 49.731 0.34 30.12 ? O2' 3AM 103 D 1 HETATM 5 C C2' 3AM . . . R 2 53.585 28.01 48.849 0.34 29.75 ? C2' 3AM 103 D 1 HETATM 6 C C3' 3AM . . . R 2 53.167 27.739 47.424 0.34 30.73 ? C3' 3AM 103 D 1 HETATM 7 O O3' 3AM . . . R 2 52.509 26.485 47.436 0.34 30.22 ? O3' 3AM 103 D 1 HETATM 8 C C1' 3AM . . . R 2 54.815 27.129 48.954 0.34 31.77 ? C1' 3AM 103 D 1 HETATM 9 O O4' 3AM . . . R 2 55.441 27.217 47.659 0.34 29.95 ? O4' 3AM 103 D 1 HETATM 10 C C4' 3AM . . . R 2 54.464 27.541 46.669 0.34 27.63 ? C4' 3AM 103 D 1 HETATM 11 C C5' 3AM . . . R 2 54.855 28.774 45.852 0.34 29.05 ? C5' 3AM 103 D 1 HETATM 12 O O5' 3AM . . . R 2 54.719 29.941 46.665 0.34 31.94 ? O5' 3AM 103 D 1 HETATM 13 N N9 3AM . . . R 2 55.84 27.5 49.954 0.34 31.76 ? N9 3AM 103 D 1 HETATM 14 C C8 3AM . . . R 2 56.424 28.705 50.109 0.34 32.03 ? C8 3AM 103 D 1 HETATM 15 N N7 3AM . . . R 2 57.361 28.664 51.09 0.34 30.57 ? N7 3AM 103 D 1 HETATM 16 C C5 3AM . . . R 2 57.402 27.403 51.555 0.34 28.15 ? C5 3AM 103 D 1 HETATM 17 C C6 3AM . . . R 2 58.17 26.672 52.594 0.34 37.81 ? C6 3AM 103 D 1 HETATM 18 N N6 3AM . . . R 2 59.113 27.29 53.352 0.34 36.26 ? N6 3AM 103 D 1 HETATM 19 C C4 3AM . . . R 2 56.405 26.64 50.796 0.34 31.51 ? C4 3AM 103 D 1 HETATM 20 N N3 3AM . . . R 2 56.226 25.329 51.068 0.34 30.07 ? N3 3AM 103 D 1 HETATM 21 C C2 3AM . . . R 2 56.96 24.728 52.023 0.34 36.73 ? C2 3AM 103 D 1 HETATM 22 N N1 3AM . . . R 2 57.89 25.362 52.764 0.34 36.06 ? N1 3AM 103 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 417 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #